Explore Workflows

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: d6000d32f6c8fbd26421a2d30d79b28901d58fb0

Packed ID: main

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/varscan_pre_and_post_processing.cwl

Branch/Commit ID: 49508a2757ff2f49f1c200774a38af1c12b531bf

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/js-expr-req-wf.cwl

Branch/Commit ID: 526f36f93655bfb098f766ff020708b5a707513a

Packed ID: wf

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file

https://github.com/datirium/workflows.git

Path: workflows/rnaseq-pe-dutp.cwl

Branch/Commit ID: 7ae3b75bbe614e59cdeaba06047234a6c40c0fe9

https://github.com/common-workflow-language/cwl-utils.git

Path: testdata/workflow_input_sf_expr_array.cwl

Branch/Commit ID: 77669d4dd1d1ebd2bdd9810f911608146d9b8e51

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/cache_test_workflow.cwl

Branch/Commit ID: d6000d32f6c8fbd26421a2d30d79b28901d58fb0

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/sum-wf.cwl

Branch/Commit ID: ae401a813472ca453a99ad067a5e6fc3bd71112b

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/duplex_alignment.cwl

Branch/Commit ID: f9600f9959acdc30259ba7e64de61104c9b01f0b

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/scatterfail.cwl

Branch/Commit ID: d6000d32f6c8fbd26421a2d30d79b28901d58fb0

Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.

https://github.com/datirium/workflows.git

Path: tools/soupx-subworkflow.cwl

Branch/Commit ID: 57437c1e9f881411b65f79acd64b7cf14df5b901